plotEIC: Plot extracted ion chromatograms from raw mzML/mzXML data

In enviGCMS: GC/LC-MS Data Analysis for Environmental Science

Plot extracted ion chromatograms from raw mzML/mzXML data

Description

Reads mzML/mzXML raw data and plots extracted ion chromatograms (EIC) for a list of target m/z values at MS1 or MS2 level. Uses RaMS for lightweight data access and plotly for interactive visualization.

Usage

plotEIC(filepath, featlist, diff = 0.005)

Arguments

filepath	character. Path to an mzML or mzXML file.
featlist	data.frame with columns: name (feature label), mz (target m/z), ms_level (either "ms1" or "ms2").
diff	numeric. Half-width of the m/z extraction window in Da. Default 0.005.

Value

A plotly object with overlaid extracted ion chromatograms.

Examples

## Not run: 
featlist <- data.frame(
  name = c("target1", "target2"),
  mz = c(300.1234, 350.5678),
  ms_level = c("ms1", "ms2")
)
plotEIC("sample.mzML", featlist)

## End(Not run)

enviGCMS documentation built on Oct. 7, 2026, 5:07 p.m.